Computational protocol: Aspergillus niger Secretes Citrate to Increase Iron Bioavailability

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Protocol publication

[…] The protein products of the expressed genes were annotated using PRIAM (Claudel-Renard et al., ), and subsequently assigned to KEGG pathway maps (Kanehisa and Goto, ; Kanehisa et al., ). Metabolic pathway enrichment analysis was performed using the hypergeometric test implementation (“phyper”) of the R software environment (R Core, ).Protein localization prediction was performed with the Softberry protComp tool (www.softberry.com). Enrichment analysis was performed on differentially expressed genes per organelle as described above. […]

Pipeline specifications

Software tools PRIAM, ProtComp
Databases KEGG PATHWAY
Application Protein sequence analysis
Organisms Aspergillus niger, Guizotia abyssinica
Chemicals Iron, Nitrogen